Atomistry » Sodium » PDB 8i1e-8ig1 » 8i6b
Atomistry »
  Sodium »
    PDB 8i1e-8ig1 »
      8i6b »

Sodium in PDB 8i6b: Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I:
3.2.2.27;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I, PDB code: 8i6b was solved by P.Raj, A.Paul, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.49 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.16, 63.68, 45.19, 90, 112.58, 90
R / Rfree (%) 14.9 / 18.2

Other elements in 8i6b:

The structure of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I (pdb code 8i6b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I, PDB code: 8i6b:

Sodium binding site 1 out of 1 in 8i6b

Go back to Sodium Binding Sites List in 8i6b
Sodium binding site 1 out of 1 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:23.0
occ:1.00
 O A:HOH431 2.7 16.7 1.0
CL A:CL309 2.8 33.9 1.0
O A:PRO56 2.9 8.7 1.0
CG2 A:VAL60 3.7 8.3 1.0
CB A:ASN59 3.7 13.3 1.0
N A:PRO56 3.8 10.6 1.0
C A:PRO56 3.8 9.8 1.0
N A:VAL60 3.8 9.4 1.0
CA A:GLY122 3.9 8.7 1.0
C A:ASN59 3.9 10.7 1.0
CB A:PHE55 3.9 10.3 1.0
O A:HOH527 3.9 22.9 1.0
C A:PHE55 4.0 10.3 1.0
CD A:PRO56 4.0 11.4 1.0
O A:ALA119 4.0 8.3 1.0
CA A:VAL60 4.1 9.3 1.0
O A:ASN59 4.2 10.7 1.0
CA A:PRO56 4.2 10.8 1.0
CA A:ASN59 4.3 11.6 1.0
O A:PHE55 4.4 10.7 1.0
N A:GLY122 4.4 8.3 1.0
C A:GLY122 4.5 7.4 1.0
O A:HOH603 4.5 40.2 1.0
CB A:VAL60 4.5 8.2 1.0
CA A:PHE55 4.5 9.7 1.0
CB A:PRO56 4.7 11.7 1.0
N A:ASN59 4.7 11.4 1.0
N A:PHE57 4.9 9.0 1.0
O A:GLY122 4.9 7.5 1.0
CG A:PRO56 4.9 12.3 1.0
O A:HOH632 5.0 30.7 0.0
CG A:ASN59 5.0 16.8 1.0
N A:VAL123 5.0 6.9 1.0

Reference:

S.Kesharwani, P.Raj, A.Paul, K.Roy, A.Bhanot, A.Mehta, A.Gopal, U.Varshney, B.Gopal, S.Sundriyal. Crystal Structures of Non-Uracil Ring Fragments in Complex with Mycobacterium Tuberculosis Uracil Dna Glycosylase (Mtung) As A Starting Point For Novel Inhibitor Design: A Case Study with the Barbituric Acid Fragment Eur.J.Med.Chem. V. 258 15604 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115604
Page generated: Wed Oct 9 12:25:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy